Starting phenix.real_space_refine on Thu Jun 12 18:01:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7k_41984/06_2025/8u7k_41984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7k_41984/06_2025/8u7k_41984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7k_41984/06_2025/8u7k_41984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7k_41984/06_2025/8u7k_41984.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7k_41984/06_2025/8u7k_41984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7k_41984/06_2025/8u7k_41984.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 63 5.16 5 C 9247 2.51 5 N 2278 2.21 5 O 2557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14147 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 6863 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 6863 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'AJP': 2, 'POV': 2} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'AJP': 2, 'POV': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 8.78, per 1000 atoms: 0.62 Number of scatterers: 14147 At special positions: 0 Unit cell: (111.78, 111.78, 133.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 2 15.00 O 2557 8.00 N 2278 7.00 C 9247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.8 seconds 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3404 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 8 sheets defined 74.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.802A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.652A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 removed outlier: 4.052A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 3.618A pdb=" N ALA A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.672A pdb=" N ALA A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 224 through 254 Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.245A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.690A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.840A pdb=" N LEU A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 376 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 381 through 414 removed outlier: 3.644A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.579A pdb=" N TRP A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.586A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 482 removed outlier: 4.134A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.985A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 4.260A pdb=" N LEU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 520' Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.752A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 621 removed outlier: 4.153A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.727A pdb=" N GLN A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.645A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 854 removed outlier: 3.731A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.175A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 954 through 958 Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1081 removed outlier: 4.170A pdb=" N THR A1081 " --> pdb=" O ILE A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1105 removed outlier: 3.791A pdb=" N ILE A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A1100 " --> pdb=" O ILE A1096 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1122 Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.670A pdb=" N LYS B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.821A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.755A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 removed outlier: 3.895A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix removed outlier: 3.597A pdb=" N ALA B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.595A pdb=" N ALA B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 224 through 254 Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.241A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 297 through 319 removed outlier: 3.696A pdb=" N ILE B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 4.075A pdb=" N LEU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 376 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 381 through 414 removed outlier: 3.693A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE B 389 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.565A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 482 removed outlier: 4.199A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 4.018A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 4.290A pdb=" N LEU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP B 520 " --> pdb=" O PHE B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 520' Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.785A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 601 Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.842A pdb=" N GLU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.547A pdb=" N GLN B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 652 removed outlier: 3.670A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 854 removed outlier: 3.728A pdb=" N LYS B 820 " --> pdb=" O ALA B 816 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 860 through 889 Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.207A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 966 through 975 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1081 removed outlier: 4.168A pdb=" N THR B1081 " --> pdb=" O ILE B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1105 removed outlier: 3.785A pdb=" N ILE B1098 " --> pdb=" O VAL B1094 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B1100 " --> pdb=" O ILE B1096 " (cutoff:3.500A) Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1122 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 4.166A pdb=" N ASN A1040 " --> pdb=" O ILE A1001 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 5.258A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 7.471A pdb=" N ARG A1185 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU A1147 " --> pdb=" O ARG A1185 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A1187 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A1145 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A1189 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 4.168A pdb=" N ASN B1040 " --> pdb=" O ILE B1001 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989 removed outlier: 5.262A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 989 " --> pdb=" O VAL B1057 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 7.472A pdb=" N ARG B1185 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU B1147 " --> pdb=" O ARG B1185 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B1187 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B1145 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B1189 " --> pdb=" O GLU B1143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137 1042 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2365 1.32 - 1.45: 3585 1.45 - 1.57: 8382 1.57 - 1.69: 4 1.69 - 1.82: 114 Bond restraints: 14450 Sorted by residual: bond pdb=" CG1 ILE A 844 " pdb=" CD1 ILE A 844 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.97e+00 bond pdb=" C26 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.375 1.409 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C45 AJP B1401 " pdb=" O44 AJP B1401 " ideal model delta sigma weight residual 1.375 1.409 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C23 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.423 1.456 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C65 AJP A1404 " pdb=" O64 AJP A1404 " ideal model delta sigma weight residual 1.373 1.406 -0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 14445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 19040 2.20 - 4.39: 557 4.39 - 6.59: 88 6.59 - 8.79: 31 8.79 - 10.98: 14 Bond angle restraints: 19730 Sorted by residual: angle pdb=" N TRP A 635 " pdb=" CA TRP A 635 " pdb=" C TRP A 635 " ideal model delta sigma weight residual 111.36 115.54 -4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" N GLN B 597 " pdb=" CA GLN B 597 " pdb=" CB GLN B 597 " ideal model delta sigma weight residual 110.22 116.07 -5.85 1.54e+00 4.22e-01 1.44e+01 angle pdb=" N GLN A 597 " pdb=" CA GLN A 597 " pdb=" CB GLN A 597 " ideal model delta sigma weight residual 110.28 116.15 -5.87 1.55e+00 4.16e-01 1.43e+01 angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 107.43 6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA GLN A 597 " pdb=" CB GLN A 597 " pdb=" CG GLN A 597 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.71: 8619 27.71 - 55.43: 383 55.43 - 83.14: 49 83.14 - 110.85: 56 110.85 - 138.57: 18 Dihedral angle restraints: 9125 sinusoidal: 3873 harmonic: 5252 Sorted by residual: dihedral pdb=" O31 AJP A1404 " pdb=" C30 AJP A1404 " pdb=" C32 AJP A1404 " pdb=" O33 AJP A1404 " ideal model delta sinusoidal sigma weight residual 177.28 38.71 138.57 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C29 AJP A1404 " pdb=" C30 AJP A1404 " pdb=" C32 AJP A1404 " pdb=" O33 AJP A1404 " ideal model delta sinusoidal sigma weight residual 299.04 162.74 136.30 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA TYR B 102 " pdb=" C TYR B 102 " pdb=" N THR B 103 " pdb=" CA THR B 103 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2066 0.066 - 0.132: 357 0.132 - 0.199: 37 0.199 - 0.265: 6 0.265 - 0.331: 1 Chirality restraints: 2467 Sorted by residual: chirality pdb=" C11 AJP B1401 " pdb=" C10 AJP B1401 " pdb=" C12 AJP B1401 " pdb=" C16 AJP B1401 " both_signs ideal model delta sigma weight residual False 2.20 2.54 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C08 AJP B1401 " pdb=" C07 AJP B1401 " pdb=" C10 AJP B1401 " pdb=" O09 AJP B1401 " both_signs ideal model delta sigma weight residual False 2.56 2.82 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C55 AJP B1401 " pdb=" C56 AJP B1401 " pdb=" O54 AJP B1401 " pdb=" O60 AJP B1401 " both_signs ideal model delta sigma weight residual False 2.13 2.37 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2464 not shown) Planarity restraints: 2377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 889 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO B 890 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 890 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 890 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 594 " 0.010 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR A 594 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 594 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 594 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 594 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 594 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 594 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 594 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 635 " -0.009 2.00e-02 2.50e+03 1.39e-02 4.82e+00 pdb=" CG TRP B 635 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 635 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 635 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 635 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 635 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 635 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 635 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 635 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 635 " 0.002 2.00e-02 2.50e+03 ... (remaining 2374 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 912 2.73 - 3.27: 15237 3.27 - 3.81: 23978 3.81 - 4.36: 25192 4.36 - 4.90: 42766 Nonbonded interactions: 108085 Sorted by model distance: nonbonded pdb=" O43 AJP A1404 " pdb=" O75 AJP A1404 " model vdw 2.182 3.040 nonbonded pdb=" OG SER A 593 " pdb=" OE1 GLU A 849 " model vdw 2.254 3.040 nonbonded pdb=" O LEU B 220 " pdb=" OG SER B 484 " model vdw 2.288 3.040 nonbonded pdb=" O LEU B 610 " pdb=" ND1 HIS B 614 " model vdw 2.295 3.120 nonbonded pdb=" O SER A 404 " pdb=" OG SER A 407 " model vdw 2.304 3.040 ... (remaining 108080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 76 through 1004 or (resid 1005 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1006 through 1191 or (resid 1402 and (nam \ e C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or n \ ame C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name O21 or name O22 or name O31 or name O32 or name C210 or name C211 or \ name C212 or name C213 or name C214)) or resid 1403)) selection = (chain 'B' and (resid 76 through 424 or (resid 425 and (name N or name CA or nam \ e C or name O or name CB )) or resid 426 through 1191 or (resid 1402 and (name C \ 1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name O21 or name O22 or name O31 or name O32 or name C210 or name C211 or nam \ e C212 or name C213 or name C214)) or resid 1403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.730 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14450 Z= 0.222 Angle : 0.923 10.982 19730 Z= 0.442 Chirality : 0.051 0.331 2467 Planarity : 0.005 0.087 2377 Dihedral : 18.927 138.565 5721 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1796 helix: 0.81 (0.14), residues: 1262 sheet: 0.22 (0.50), residues: 110 loop : -0.49 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 635 HIS 0.014 0.001 HIS B 350 PHE 0.036 0.002 PHE B 455 TYR 0.046 0.002 TYR A 594 ARG 0.009 0.001 ARG A 875 Details of bonding type rmsd hydrogen bonds : bond 0.11604 ( 1042) hydrogen bonds : angle 5.35362 ( 3078) covalent geometry : bond 0.00485 (14450) covalent geometry : angle 0.92317 (19730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8615 (pmm) cc_final: 0.8344 (pmm) REVERT: A 199 MET cc_start: 0.8519 (ttt) cc_final: 0.8100 (ttt) REVERT: A 201 PHE cc_start: 0.9118 (t80) cc_final: 0.8598 (t80) REVERT: A 205 MET cc_start: 0.8054 (mpp) cc_final: 0.7404 (mpp) REVERT: A 231 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 240 CYS cc_start: 0.8778 (m) cc_final: 0.8302 (m) REVERT: A 268 PHE cc_start: 0.8614 (t80) cc_final: 0.8231 (t80) REVERT: A 524 ASP cc_start: 0.8967 (p0) cc_final: 0.8388 (p0) REVERT: A 586 MET cc_start: 0.8451 (ptp) cc_final: 0.8060 (ptp) REVERT: A 643 TRP cc_start: 0.6789 (t60) cc_final: 0.6254 (t-100) REVERT: B 231 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 240 CYS cc_start: 0.8779 (m) cc_final: 0.8307 (m) REVERT: B 268 PHE cc_start: 0.8594 (t80) cc_final: 0.8216 (t80) REVERT: B 370 VAL cc_start: 0.9397 (p) cc_final: 0.9113 (t) REVERT: B 524 ASP cc_start: 0.9009 (p0) cc_final: 0.8464 (p0) REVERT: B 586 MET cc_start: 0.8401 (ptp) cc_final: 0.8069 (ptp) REVERT: B 924 GLU cc_start: 0.8601 (pp20) cc_final: 0.8257 (pp20) REVERT: B 925 MET cc_start: 0.9091 (mmp) cc_final: 0.8852 (mmm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2368 time to fit residues: 108.5371 Evaluate side-chains 226 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 0.0870 chunk 46 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 overall best weight: 4.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.100905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.073187 restraints weight = 44257.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.071871 restraints weight = 40281.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.072474 restraints weight = 34614.291| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14450 Z= 0.227 Angle : 0.761 8.136 19730 Z= 0.371 Chirality : 0.043 0.248 2467 Planarity : 0.004 0.059 2377 Dihedral : 14.711 138.280 2752 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1796 helix: 1.15 (0.14), residues: 1302 sheet: 0.10 (0.48), residues: 110 loop : -0.63 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 635 HIS 0.004 0.001 HIS A 350 PHE 0.020 0.002 PHE B 248 TYR 0.031 0.002 TYR A 309 ARG 0.003 0.000 ARG A 875 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 1042) hydrogen bonds : angle 4.43756 ( 3078) covalent geometry : bond 0.00490 (14450) covalent geometry : angle 0.76139 (19730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8372 (pmm) cc_final: 0.7931 (pmm) REVERT: A 199 MET cc_start: 0.8543 (ttt) cc_final: 0.8061 (ttt) REVERT: A 201 PHE cc_start: 0.9105 (t80) cc_final: 0.8512 (t80) REVERT: A 205 MET cc_start: 0.8046 (mpp) cc_final: 0.7230 (mpp) REVERT: A 240 CYS cc_start: 0.8871 (m) cc_final: 0.8430 (m) REVERT: A 366 MET cc_start: 0.7796 (ttm) cc_final: 0.7529 (ttm) REVERT: A 401 MET cc_start: 0.9071 (ptm) cc_final: 0.8767 (ptm) REVERT: A 524 ASP cc_start: 0.9181 (p0) cc_final: 0.8545 (p0) REVERT: A 586 MET cc_start: 0.8474 (ptp) cc_final: 0.8077 (ptp) REVERT: A 643 TRP cc_start: 0.6855 (t60) cc_final: 0.6417 (t-100) REVERT: A 853 ILE cc_start: 0.9166 (tp) cc_final: 0.8889 (tp) REVERT: B 160 MET cc_start: 0.8124 (ptm) cc_final: 0.7811 (ptt) REVERT: B 233 GLU cc_start: 0.8424 (tp30) cc_final: 0.8147 (tp30) REVERT: B 240 CYS cc_start: 0.8792 (m) cc_final: 0.8346 (m) REVERT: B 268 PHE cc_start: 0.8652 (t80) cc_final: 0.8238 (t80) REVERT: B 524 ASP cc_start: 0.9193 (p0) cc_final: 0.8583 (p0) REVERT: B 578 MET cc_start: 0.8461 (ppp) cc_final: 0.8248 (ppp) REVERT: B 586 MET cc_start: 0.8457 (ptp) cc_final: 0.8115 (ptt) REVERT: B 597 GLN cc_start: 0.8808 (mp10) cc_final: 0.8511 (mp10) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2203 time to fit residues: 93.3988 Evaluate side-chains 216 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 75 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.074854 restraints weight = 44341.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.074098 restraints weight = 36485.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074837 restraints weight = 34710.688| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14450 Z= 0.134 Angle : 0.673 8.645 19730 Z= 0.326 Chirality : 0.040 0.232 2467 Planarity : 0.004 0.048 2377 Dihedral : 12.345 137.288 2752 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1796 helix: 1.42 (0.14), residues: 1292 sheet: 0.09 (0.47), residues: 110 loop : -0.66 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 635 HIS 0.005 0.001 HIS A 350 PHE 0.018 0.001 PHE B 406 TYR 0.041 0.001 TYR A 594 ARG 0.005 0.000 ARG B 875 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 1042) hydrogen bonds : angle 4.12688 ( 3078) covalent geometry : bond 0.00279 (14450) covalent geometry : angle 0.67330 (19730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8067 (pp20) cc_final: 0.7705 (pt0) REVERT: A 133 MET cc_start: 0.8288 (pmm) cc_final: 0.7840 (pmm) REVERT: A 199 MET cc_start: 0.8485 (ttt) cc_final: 0.7927 (ttt) REVERT: A 233 GLU cc_start: 0.8413 (tp30) cc_final: 0.8151 (tp30) REVERT: A 235 LEU cc_start: 0.9404 (tp) cc_final: 0.9199 (tp) REVERT: A 240 CYS cc_start: 0.8767 (m) cc_final: 0.8356 (m) REVERT: A 366 MET cc_start: 0.7536 (ttm) cc_final: 0.7174 (ttm) REVERT: A 401 MET cc_start: 0.8937 (ptm) cc_final: 0.8652 (ptm) REVERT: A 524 ASP cc_start: 0.9209 (p0) cc_final: 0.8547 (p0) REVERT: A 586 MET cc_start: 0.8461 (ptp) cc_final: 0.8035 (ptp) REVERT: A 594 TYR cc_start: 0.9492 (m-80) cc_final: 0.9247 (m-80) REVERT: A 643 TRP cc_start: 0.6835 (t60) cc_final: 0.6404 (t-100) REVERT: A 853 ILE cc_start: 0.9160 (tp) cc_final: 0.8908 (tp) REVERT: A 899 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7868 (ttm-80) REVERT: B 160 MET cc_start: 0.8075 (ptm) cc_final: 0.7774 (ptt) REVERT: B 233 GLU cc_start: 0.8624 (tp30) cc_final: 0.8291 (tp30) REVERT: B 240 CYS cc_start: 0.8751 (m) cc_final: 0.8301 (m) REVERT: B 268 PHE cc_start: 0.8632 (t80) cc_final: 0.8252 (t80) REVERT: B 524 ASP cc_start: 0.9191 (p0) cc_final: 0.8520 (p0) REVERT: B 578 MET cc_start: 0.8468 (ppp) cc_final: 0.8254 (ppp) REVERT: B 586 MET cc_start: 0.8431 (ptp) cc_final: 0.8078 (ptp) REVERT: B 612 VAL cc_start: 0.9413 (m) cc_final: 0.9169 (m) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2217 time to fit residues: 102.6547 Evaluate side-chains 240 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 66 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 82 optimal weight: 0.0670 chunk 160 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 40 optimal weight: 0.0470 chunk 50 optimal weight: 9.9990 chunk 92 optimal weight: 0.0370 chunk 152 optimal weight: 2.9990 overall best weight: 0.7696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075109 restraints weight = 43817.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.076744 restraints weight = 29527.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.076791 restraints weight = 22557.071| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14450 Z= 0.123 Angle : 0.661 8.867 19730 Z= 0.317 Chirality : 0.040 0.242 2467 Planarity : 0.004 0.044 2377 Dihedral : 11.249 136.664 2752 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1796 helix: 1.55 (0.14), residues: 1292 sheet: 0.13 (0.46), residues: 110 loop : -0.52 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 635 HIS 0.014 0.001 HIS B 350 PHE 0.015 0.001 PHE B 248 TYR 0.024 0.001 TYR A 594 ARG 0.001 0.000 ARG B 875 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 1042) hydrogen bonds : angle 3.99523 ( 3078) covalent geometry : bond 0.00245 (14450) covalent geometry : angle 0.66055 (19730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8218 (ptm) cc_final: 0.7887 (ptt) REVERT: A 199 MET cc_start: 0.8459 (ttt) cc_final: 0.8158 (ttt) REVERT: A 233 GLU cc_start: 0.8458 (tp30) cc_final: 0.8109 (tp30) REVERT: A 240 CYS cc_start: 0.8797 (m) cc_final: 0.8390 (m) REVERT: A 366 MET cc_start: 0.7623 (ttm) cc_final: 0.7333 (ttm) REVERT: A 401 MET cc_start: 0.9013 (ptm) cc_final: 0.8693 (ptm) REVERT: A 524 ASP cc_start: 0.9188 (p0) cc_final: 0.8515 (p0) REVERT: A 586 MET cc_start: 0.8368 (ptp) cc_final: 0.8055 (ptp) REVERT: A 594 TYR cc_start: 0.9567 (m-80) cc_final: 0.9182 (m-80) REVERT: A 643 TRP cc_start: 0.6834 (t60) cc_final: 0.6391 (t-100) REVERT: A 853 ILE cc_start: 0.9154 (tp) cc_final: 0.8885 (tp) REVERT: A 899 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7877 (ttm-80) REVERT: B 160 MET cc_start: 0.8245 (ptm) cc_final: 0.7976 (ptt) REVERT: B 233 GLU cc_start: 0.8564 (tp30) cc_final: 0.8160 (tp30) REVERT: B 240 CYS cc_start: 0.8790 (m) cc_final: 0.8347 (m) REVERT: B 268 PHE cc_start: 0.8646 (t80) cc_final: 0.8290 (t80) REVERT: B 524 ASP cc_start: 0.9181 (p0) cc_final: 0.8524 (p0) REVERT: B 586 MET cc_start: 0.8491 (ptp) cc_final: 0.8130 (ptp) REVERT: B 588 LYS cc_start: 0.9439 (ptpp) cc_final: 0.9188 (ptpp) REVERT: B 612 VAL cc_start: 0.9485 (m) cc_final: 0.9247 (m) REVERT: B 853 ILE cc_start: 0.9258 (tp) cc_final: 0.8951 (tp) REVERT: B 912 THR cc_start: 0.9057 (t) cc_final: 0.8781 (t) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2559 time to fit residues: 126.5207 Evaluate side-chains 249 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 0.0050 chunk 135 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.102542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.073611 restraints weight = 44707.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.072162 restraints weight = 31974.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.072927 restraints weight = 28460.384| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14450 Z= 0.154 Angle : 0.677 8.687 19730 Z= 0.328 Chirality : 0.041 0.251 2467 Planarity : 0.004 0.047 2377 Dihedral : 10.839 137.024 2752 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1796 helix: 1.55 (0.14), residues: 1294 sheet: 0.17 (0.47), residues: 110 loop : -0.61 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 635 HIS 0.009 0.001 HIS A 350 PHE 0.014 0.001 PHE A 365 TYR 0.026 0.001 TYR A 309 ARG 0.005 0.000 ARG B 865 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 1042) hydrogen bonds : angle 4.03072 ( 3078) covalent geometry : bond 0.00336 (14450) covalent geometry : angle 0.67695 (19730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8546 (ttt) cc_final: 0.8141 (ttt) REVERT: A 233 GLU cc_start: 0.8651 (tp30) cc_final: 0.8268 (tp30) REVERT: A 240 CYS cc_start: 0.8813 (m) cc_final: 0.8394 (m) REVERT: A 366 MET cc_start: 0.7635 (ttm) cc_final: 0.7388 (ttm) REVERT: A 401 MET cc_start: 0.9059 (ptm) cc_final: 0.8724 (ptm) REVERT: A 524 ASP cc_start: 0.9240 (p0) cc_final: 0.8603 (p0) REVERT: A 586 MET cc_start: 0.8423 (ptp) cc_final: 0.8141 (ptp) REVERT: A 590 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8402 (mt-10) REVERT: A 594 TYR cc_start: 0.9536 (m-80) cc_final: 0.9104 (m-80) REVERT: A 643 TRP cc_start: 0.6917 (t60) cc_final: 0.6458 (t-100) REVERT: A 853 ILE cc_start: 0.9212 (tp) cc_final: 0.8952 (tp) REVERT: A 899 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7933 (ttm170) REVERT: A 911 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 124 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7345 (mp0) REVERT: B 160 MET cc_start: 0.8324 (ptm) cc_final: 0.8049 (ptt) REVERT: B 233 GLU cc_start: 0.8604 (tp30) cc_final: 0.8333 (tp30) REVERT: B 240 CYS cc_start: 0.8828 (m) cc_final: 0.8382 (m) REVERT: B 268 PHE cc_start: 0.8745 (t80) cc_final: 0.8367 (t80) REVERT: B 462 ILE cc_start: 0.9359 (tp) cc_final: 0.9040 (mm) REVERT: B 524 ASP cc_start: 0.9224 (p0) cc_final: 0.8593 (p0) REVERT: B 586 MET cc_start: 0.8549 (ptp) cc_final: 0.8267 (ptt) REVERT: B 588 LYS cc_start: 0.9449 (ptpp) cc_final: 0.9230 (pttm) REVERT: B 590 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8411 (mt-10) REVERT: B 610 LEU cc_start: 0.9451 (tt) cc_final: 0.8824 (tp) REVERT: B 614 HIS cc_start: 0.8444 (m-70) cc_final: 0.8133 (m-70) REVERT: B 838 ASP cc_start: 0.9011 (t0) cc_final: 0.8799 (t0) REVERT: B 853 ILE cc_start: 0.9320 (tp) cc_final: 0.9030 (tp) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.2190 time to fit residues: 104.9531 Evaluate side-chains 250 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 146 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075217 restraints weight = 44698.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.075636 restraints weight = 30927.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.077824 restraints weight = 21774.684| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14450 Z= 0.123 Angle : 0.677 9.029 19730 Z= 0.325 Chirality : 0.041 0.290 2467 Planarity : 0.004 0.043 2377 Dihedral : 10.229 136.396 2752 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1796 helix: 1.59 (0.14), residues: 1294 sheet: 0.16 (0.47), residues: 108 loop : -0.53 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP B 635 HIS 0.007 0.001 HIS B 614 PHE 0.017 0.001 PHE B 248 TYR 0.021 0.001 TYR A 309 ARG 0.003 0.000 ARG B 583 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 1042) hydrogen bonds : angle 3.96003 ( 3078) covalent geometry : bond 0.00247 (14450) covalent geometry : angle 0.67742 (19730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7279 (mt-10) REVERT: A 133 MET cc_start: 0.8345 (pmm) cc_final: 0.7647 (pmm) REVERT: A 199 MET cc_start: 0.8399 (ttt) cc_final: 0.7972 (ttt) REVERT: A 233 GLU cc_start: 0.8536 (tp30) cc_final: 0.8130 (tp30) REVERT: A 240 CYS cc_start: 0.8711 (m) cc_final: 0.8337 (m) REVERT: A 366 MET cc_start: 0.7732 (ttm) cc_final: 0.7424 (ttm) REVERT: A 383 MET cc_start: 0.8338 (tmm) cc_final: 0.7938 (tmm) REVERT: A 401 MET cc_start: 0.8942 (ptm) cc_final: 0.8617 (ptm) REVERT: A 524 ASP cc_start: 0.9143 (p0) cc_final: 0.8439 (p0) REVERT: A 586 MET cc_start: 0.8455 (ptp) cc_final: 0.8042 (ptp) REVERT: A 590 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 594 TYR cc_start: 0.9482 (m-80) cc_final: 0.8989 (m-80) REVERT: A 633 LYS cc_start: 0.9361 (pttp) cc_final: 0.8884 (mtpt) REVERT: A 838 ASP cc_start: 0.8906 (t0) cc_final: 0.8696 (t0) REVERT: A 853 ILE cc_start: 0.9100 (tp) cc_final: 0.8807 (tp) REVERT: A 899 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: A 912 THR cc_start: 0.8075 (m) cc_final: 0.7764 (m) REVERT: A 923 ASP cc_start: 0.7337 (t0) cc_final: 0.6943 (t0) REVERT: B 160 MET cc_start: 0.8294 (ptm) cc_final: 0.8011 (ptt) REVERT: B 233 GLU cc_start: 0.8603 (tp30) cc_final: 0.8280 (tp30) REVERT: B 240 CYS cc_start: 0.8714 (m) cc_final: 0.8303 (m) REVERT: B 268 PHE cc_start: 0.8625 (t80) cc_final: 0.8270 (t80) REVERT: B 346 GLU cc_start: 0.8050 (pp20) cc_final: 0.7751 (pp20) REVERT: B 524 ASP cc_start: 0.9121 (p0) cc_final: 0.8446 (p0) REVERT: B 586 MET cc_start: 0.8490 (ptp) cc_final: 0.8096 (ptp) REVERT: B 588 LYS cc_start: 0.9449 (ptpp) cc_final: 0.9218 (ptpp) REVERT: B 590 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8406 (mt-10) REVERT: B 594 TYR cc_start: 0.9303 (m-80) cc_final: 0.8739 (m-80) REVERT: B 608 LEU cc_start: 0.9401 (tp) cc_final: 0.9166 (tt) REVERT: B 614 HIS cc_start: 0.8376 (m90) cc_final: 0.8126 (m90) REVERT: B 853 ILE cc_start: 0.9198 (tp) cc_final: 0.8888 (tp) REVERT: B 912 THR cc_start: 0.9040 (t) cc_final: 0.8796 (t) REVERT: B 923 ASP cc_start: 0.7282 (t0) cc_final: 0.7044 (t0) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2125 time to fit residues: 106.8904 Evaluate side-chains 260 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.069565 restraints weight = 44854.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.071813 restraints weight = 24139.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073247 restraints weight = 16665.098| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14450 Z= 0.147 Angle : 0.688 9.386 19730 Z= 0.335 Chirality : 0.041 0.300 2467 Planarity : 0.004 0.052 2377 Dihedral : 9.996 136.874 2752 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.20), residues: 1796 helix: 1.59 (0.14), residues: 1294 sheet: 0.17 (0.48), residues: 108 loop : -0.50 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 635 HIS 0.003 0.001 HIS B 614 PHE 0.024 0.001 PHE B 365 TYR 0.026 0.001 TYR A 387 ARG 0.003 0.000 ARG B 583 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 1042) hydrogen bonds : angle 4.02198 ( 3078) covalent geometry : bond 0.00318 (14450) covalent geometry : angle 0.68790 (19730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8443 (ttt) cc_final: 0.8004 (ttt) REVERT: A 233 GLU cc_start: 0.8591 (tp30) cc_final: 0.8311 (tp30) REVERT: A 240 CYS cc_start: 0.8775 (m) cc_final: 0.8370 (m) REVERT: A 366 MET cc_start: 0.7728 (ttm) cc_final: 0.7463 (ttm) REVERT: A 387 TYR cc_start: 0.7424 (m-80) cc_final: 0.6894 (m-80) REVERT: A 401 MET cc_start: 0.9002 (ptm) cc_final: 0.8649 (ptm) REVERT: A 524 ASP cc_start: 0.9162 (p0) cc_final: 0.8462 (p0) REVERT: A 586 MET cc_start: 0.8595 (ptp) cc_final: 0.8195 (ptp) REVERT: A 590 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8411 (mt-10) REVERT: A 594 TYR cc_start: 0.9548 (m-80) cc_final: 0.9204 (m-10) REVERT: A 843 TYR cc_start: 0.9174 (t80) cc_final: 0.8853 (t80) REVERT: A 847 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 853 ILE cc_start: 0.9060 (tp) cc_final: 0.8775 (tp) REVERT: A 899 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8014 (ttm170) REVERT: A 912 THR cc_start: 0.8169 (m) cc_final: 0.7808 (m) REVERT: A 923 ASP cc_start: 0.7502 (t0) cc_final: 0.7222 (t0) REVERT: A 941 LEU cc_start: 0.8767 (tt) cc_final: 0.8565 (tt) REVERT: B 160 MET cc_start: 0.8324 (ptm) cc_final: 0.8038 (ptt) REVERT: B 233 GLU cc_start: 0.8583 (tp30) cc_final: 0.8212 (tp30) REVERT: B 240 CYS cc_start: 0.8826 (m) cc_final: 0.8394 (m) REVERT: B 268 PHE cc_start: 0.8636 (t80) cc_final: 0.8294 (t80) REVERT: B 346 GLU cc_start: 0.8197 (pp20) cc_final: 0.7946 (pp20) REVERT: B 524 ASP cc_start: 0.9146 (p0) cc_final: 0.8459 (p0) REVERT: B 586 MET cc_start: 0.8617 (ptp) cc_final: 0.8271 (ptt) REVERT: B 588 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9284 (pttm) REVERT: B 590 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8483 (mt-10) REVERT: B 614 HIS cc_start: 0.8315 (m90) cc_final: 0.8049 (m-70) REVERT: B 838 ASP cc_start: 0.9126 (t0) cc_final: 0.8868 (t0) REVERT: B 853 ILE cc_start: 0.9181 (tp) cc_final: 0.8851 (tp) REVERT: B 912 THR cc_start: 0.9121 (t) cc_final: 0.8718 (t) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2169 time to fit residues: 104.3822 Evaluate side-chains 252 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.102917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073508 restraints weight = 44790.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.075053 restraints weight = 31959.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075352 restraints weight = 22399.260| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14450 Z= 0.159 Angle : 0.705 8.243 19730 Z= 0.347 Chirality : 0.042 0.293 2467 Planarity : 0.004 0.046 2377 Dihedral : 9.884 137.061 2752 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.07 % Allowed : 1.13 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1796 helix: 1.53 (0.14), residues: 1294 sheet: 0.13 (0.47), residues: 108 loop : -0.49 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 635 HIS 0.003 0.001 HIS A 614 PHE 0.021 0.001 PHE B 406 TYR 0.024 0.001 TYR A 309 ARG 0.003 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 1042) hydrogen bonds : angle 4.14171 ( 3078) covalent geometry : bond 0.00349 (14450) covalent geometry : angle 0.70473 (19730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7080 (mt-10) REVERT: A 199 MET cc_start: 0.8499 (ttt) cc_final: 0.8088 (ttt) REVERT: A 233 GLU cc_start: 0.8505 (tp30) cc_final: 0.8220 (tp30) REVERT: A 240 CYS cc_start: 0.8798 (m) cc_final: 0.8399 (m) REVERT: A 366 MET cc_start: 0.7740 (ttm) cc_final: 0.7486 (ttm) REVERT: A 401 MET cc_start: 0.8979 (ptm) cc_final: 0.8640 (ptm) REVERT: A 524 ASP cc_start: 0.9211 (p0) cc_final: 0.8571 (p0) REVERT: A 586 MET cc_start: 0.8466 (ptp) cc_final: 0.8106 (ptp) REVERT: A 590 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8310 (mt-10) REVERT: A 594 TYR cc_start: 0.9455 (m-80) cc_final: 0.9117 (m-10) REVERT: A 613 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8788 (pp30) REVERT: A 853 ILE cc_start: 0.9134 (tp) cc_final: 0.8823 (tp) REVERT: A 857 MET cc_start: 0.8815 (tpt) cc_final: 0.8122 (tmm) REVERT: A 899 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.7959 (ttm170) REVERT: B 160 MET cc_start: 0.8297 (ptm) cc_final: 0.8024 (ptt) REVERT: B 233 GLU cc_start: 0.8471 (tp30) cc_final: 0.8082 (tp30) REVERT: B 240 CYS cc_start: 0.8771 (m) cc_final: 0.8343 (m) REVERT: B 268 PHE cc_start: 0.8687 (t80) cc_final: 0.8340 (t80) REVERT: B 346 GLU cc_start: 0.8211 (pp20) cc_final: 0.7956 (pp20) REVERT: B 524 ASP cc_start: 0.9198 (p0) cc_final: 0.8568 (p0) REVERT: B 586 MET cc_start: 0.8503 (ptp) cc_final: 0.8160 (ptt) REVERT: B 588 LYS cc_start: 0.9432 (ptpp) cc_final: 0.9215 (pttm) REVERT: B 614 HIS cc_start: 0.8296 (m90) cc_final: 0.8054 (m-70) REVERT: B 643 TRP cc_start: 0.6979 (t-100) cc_final: 0.6751 (t-100) REVERT: B 853 ILE cc_start: 0.9225 (tp) cc_final: 0.8909 (tp) REVERT: B 912 THR cc_start: 0.9183 (t) cc_final: 0.8784 (t) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.2135 time to fit residues: 101.2848 Evaluate side-chains 242 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 0.0040 chunk 126 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 162 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.103564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075798 restraints weight = 44092.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.076518 restraints weight = 33219.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.076906 restraints weight = 25426.176| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14450 Z= 0.139 Angle : 0.704 11.062 19730 Z= 0.343 Chirality : 0.042 0.298 2467 Planarity : 0.004 0.051 2377 Dihedral : 9.661 136.803 2752 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1796 helix: 1.53 (0.14), residues: 1296 sheet: 0.14 (0.47), residues: 108 loop : -0.45 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.002 TRP B 635 HIS 0.002 0.001 HIS A 350 PHE 0.016 0.001 PHE B 248 TYR 0.024 0.001 TYR A 309 ARG 0.002 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1042) hydrogen bonds : angle 4.10967 ( 3078) covalent geometry : bond 0.00297 (14450) covalent geometry : angle 0.70448 (19730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7084 (mt-10) REVERT: A 133 MET cc_start: 0.8391 (pmm) cc_final: 0.8162 (pmm) REVERT: A 199 MET cc_start: 0.8444 (ttt) cc_final: 0.8029 (ttt) REVERT: A 233 GLU cc_start: 0.8486 (tp30) cc_final: 0.8179 (tp30) REVERT: A 240 CYS cc_start: 0.8767 (m) cc_final: 0.8346 (m) REVERT: A 366 MET cc_start: 0.7728 (ttm) cc_final: 0.7445 (ttm) REVERT: A 387 TYR cc_start: 0.7220 (m-80) cc_final: 0.6877 (m-80) REVERT: A 401 MET cc_start: 0.8950 (ptm) cc_final: 0.8624 (ptm) REVERT: A 524 ASP cc_start: 0.9183 (p0) cc_final: 0.8532 (p0) REVERT: A 586 MET cc_start: 0.8477 (ptp) cc_final: 0.8120 (ptp) REVERT: A 590 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 594 TYR cc_start: 0.9464 (m-80) cc_final: 0.9130 (m-10) REVERT: A 838 ASP cc_start: 0.8920 (t0) cc_final: 0.8719 (t0) REVERT: A 843 TYR cc_start: 0.8990 (t80) cc_final: 0.8727 (t80) REVERT: A 853 ILE cc_start: 0.9084 (tp) cc_final: 0.8789 (tp) REVERT: A 857 MET cc_start: 0.8949 (tpt) cc_final: 0.8255 (tmm) REVERT: A 899 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.7956 (ttm170) REVERT: A 912 THR cc_start: 0.8160 (m) cc_final: 0.7831 (m) REVERT: B 160 MET cc_start: 0.8290 (ptm) cc_final: 0.8008 (ptt) REVERT: B 233 GLU cc_start: 0.8396 (tp30) cc_final: 0.8003 (tp30) REVERT: B 240 CYS cc_start: 0.8782 (m) cc_final: 0.8355 (m) REVERT: B 268 PHE cc_start: 0.8658 (t80) cc_final: 0.8318 (t80) REVERT: B 346 GLU cc_start: 0.8128 (pp20) cc_final: 0.7866 (pp20) REVERT: B 483 MET cc_start: 0.8477 (pmm) cc_final: 0.8242 (pmm) REVERT: B 524 ASP cc_start: 0.9182 (p0) cc_final: 0.8536 (p0) REVERT: B 586 MET cc_start: 0.8485 (ptp) cc_final: 0.8190 (ptt) REVERT: B 588 LYS cc_start: 0.9439 (ptpp) cc_final: 0.9221 (pttm) REVERT: B 590 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 614 HIS cc_start: 0.8235 (m90) cc_final: 0.7978 (m90) REVERT: B 643 TRP cc_start: 0.6916 (t-100) cc_final: 0.6695 (t-100) REVERT: B 838 ASP cc_start: 0.8980 (t0) cc_final: 0.8764 (t0) REVERT: B 853 ILE cc_start: 0.9200 (tp) cc_final: 0.8875 (tp) REVERT: B 912 THR cc_start: 0.9141 (t) cc_final: 0.8781 (t) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2722 time to fit residues: 130.0166 Evaluate side-chains 245 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 164 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 162 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 chunk 138 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075814 restraints weight = 44080.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074448 restraints weight = 38978.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075149 restraints weight = 35207.118| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14450 Z= 0.144 Angle : 0.715 10.578 19730 Z= 0.349 Chirality : 0.042 0.300 2467 Planarity : 0.004 0.050 2377 Dihedral : 9.507 136.843 2752 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.20), residues: 1796 helix: 1.49 (0.14), residues: 1296 sheet: 0.14 (0.48), residues: 108 loop : -0.45 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP B 635 HIS 0.002 0.001 HIS A 614 PHE 0.014 0.001 PHE B 95 TYR 0.024 0.001 TYR A 309 ARG 0.013 0.000 ARG A 865 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 1042) hydrogen bonds : angle 4.13037 ( 3078) covalent geometry : bond 0.00313 (14450) covalent geometry : angle 0.71464 (19730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 154 MET cc_start: 0.8550 (tpp) cc_final: 0.7999 (tpt) REVERT: A 233 GLU cc_start: 0.8448 (tp30) cc_final: 0.8170 (tp30) REVERT: A 240 CYS cc_start: 0.8742 (m) cc_final: 0.8346 (m) REVERT: A 366 MET cc_start: 0.7701 (ttm) cc_final: 0.7498 (ttm) REVERT: A 387 TYR cc_start: 0.7248 (m-80) cc_final: 0.6948 (m-10) REVERT: A 401 MET cc_start: 0.8948 (ptm) cc_final: 0.8615 (ptm) REVERT: A 524 ASP cc_start: 0.9244 (p0) cc_final: 0.8605 (p0) REVERT: A 586 MET cc_start: 0.8358 (ptp) cc_final: 0.7993 (ptp) REVERT: A 590 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 594 TYR cc_start: 0.9421 (m-80) cc_final: 0.8904 (m-80) REVERT: A 843 TYR cc_start: 0.8865 (t80) cc_final: 0.8589 (t80) REVERT: A 853 ILE cc_start: 0.9092 (tp) cc_final: 0.8781 (tp) REVERT: A 857 MET cc_start: 0.8949 (tpt) cc_final: 0.8265 (tmm) REVERT: A 899 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.7910 (ttm170) REVERT: A 912 THR cc_start: 0.8174 (m) cc_final: 0.7863 (m) REVERT: B 160 MET cc_start: 0.8150 (ptm) cc_final: 0.7877 (ptt) REVERT: B 233 GLU cc_start: 0.8360 (tp30) cc_final: 0.7971 (tp30) REVERT: B 240 CYS cc_start: 0.8725 (m) cc_final: 0.8315 (m) REVERT: B 268 PHE cc_start: 0.8624 (t80) cc_final: 0.8273 (t80) REVERT: B 346 GLU cc_start: 0.8222 (pp20) cc_final: 0.7923 (pp20) REVERT: B 483 MET cc_start: 0.8482 (pmm) cc_final: 0.8209 (pmm) REVERT: B 524 ASP cc_start: 0.9225 (p0) cc_final: 0.8585 (p0) REVERT: B 586 MET cc_start: 0.8431 (ptp) cc_final: 0.8154 (ptt) REVERT: B 614 HIS cc_start: 0.8134 (m90) cc_final: 0.7929 (m90) REVERT: B 853 ILE cc_start: 0.9149 (tp) cc_final: 0.8816 (tp) REVERT: B 912 THR cc_start: 0.9178 (t) cc_final: 0.8860 (t) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2245 time to fit residues: 105.3249 Evaluate side-chains 242 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 5.9990 chunk 178 optimal weight: 40.0000 chunk 164 optimal weight: 20.0000 chunk 131 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS A 928 HIS B 928 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.104227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.075846 restraints weight = 44956.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.076778 restraints weight = 32837.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076776 restraints weight = 26612.558| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14450 Z= 0.128 Angle : 0.709 10.437 19730 Z= 0.344 Chirality : 0.042 0.303 2467 Planarity : 0.004 0.051 2377 Dihedral : 9.089 136.298 2752 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1796 helix: 1.54 (0.14), residues: 1296 sheet: 0.21 (0.48), residues: 108 loop : -0.45 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP B 635 HIS 0.003 0.000 HIS A 928 PHE 0.023 0.001 PHE B 248 TYR 0.021 0.001 TYR A 309 ARG 0.008 0.000 ARG A 865 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 1042) hydrogen bonds : angle 4.05305 ( 3078) covalent geometry : bond 0.00267 (14450) covalent geometry : angle 0.70890 (19730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4315.39 seconds wall clock time: 77 minutes 49.72 seconds (4669.72 seconds total)